Lineage assignment

Pangolin and Nextclade

Lineage assigment table using Pangolin and Nextclade of all samples.

Sample Coverage Pangolin Scorpio Nextclade WHO clade Note
Coinfection-nanopore2020-20%-error-20%-minor-variant 99.31% B.1.1.529 NA B.1.1 NA Usher placements: B.1.1.529(1/1)
Coinfection-nanopore2020-2%-error-5%-minor-variant 98.67% BA.2 Omicron (BA.2-like) BA.2 Omicron Usher placements: BA.2(1/1)
Coinfection-nanopore2020-5%-error-50%-minor-variant 99.29% B.1.1.529 NA B.1.617.2 Delta Usher placements: B.1.1.529(1/1)
Coinfection-nanopore2020-10%-error-20%-minor-variant 99.32% B.1.1.529 NA B.1.1 NA Usher placements: B.1.1.529(1/1)
Coinfection-nanopore2020-2%-error-10%-minor-variant 99.44% BA.2 Probable Omicron (Unassigned) BA.2 Omicron Usher placements: BA.2(1/1); scorpio found insufficient support to assign a specific lineage
Coinfection-nanopore2020-10%-error-50%-minor-variant 99.29% B.1.1.529 NA B.1.617.2 Delta Usher placements: B.1.1.529(1/1)
Coinfection-nanopore2020-5%-error-20%-minor-variant 99.3% B.1.1.529 NA B.1.1 NA Usher placements: B.1.1.529(1/1)
Coinfection-nanopore2020-5%-error-10%-minor-variant 99.41% BA.2 Probable Omicron (Unassigned) BA.2 Omicron Usher placements: BA.2(1/1); scorpio found insufficient support to assign a specific lineage
Coinfection-nanopore2020-20%-error-10%-minor-variant 99.49% BA.2 Omicron (Unassigned) BA.2 Omicron Usher placements: BA.2(3/3); scorpio found insufficient support to assign a specific lineage
Coinfection-nanopore2020-2%-error-50%-minor-variant 99.28% B.1.1.529 NA B.1.617.2 Delta Usher placements: B.1.1.529(1/2) B.1.617.2(1/2)
Coinfection-nanopore2020-20%-error-50%-minor-variant 99.28% B.1.1.529 NA B.1.617.2 Delta Usher placements: B.1.1.529(1/1)
Coinfection-nanopore2020-5%-error-5%-minor-variant 99.55% BA.2 Omicron (BA.2-like) BA.2 Omicron Usher placements: BA.2(2/2)
Coinfection-nanopore2020-2%-error-2%-minor-variant 98.56% BA.2 Omicron (BA.2-like) BA.2 Omicron Usher placements: BA.2(2/2)
Coinfection-nanopore2020-10%-error-2%-minor-variant 99.44% BA.2 Omicron (BA.2-like) BA.2 Omicron Usher placements: BA.2(2/2)
Coinfection-nanopore2020-10%-error-5%-minor-variant 99.51% BA.2 Omicron (BA.2-like) BA.2 Omicron Usher placements: BA.2(2/2)
Coinfection-nanopore2020-10%-error-10%-minor-variant 99.51% BA.2 Omicron (Unassigned) BA.2 Omicron Usher placements: BA.2(2/2); scorpio found insufficient support to assign a specific lineage
Coinfection-nanopore2020-20%-error-5%-minor-variant 99.52% BA.2 Omicron (BA.2-like) BA.2 Omicron Usher placements: BA.2(2/2)
Coinfection-nanopore2020-5%-error-2%-minor-variant 99.51% BA.2 Omicron (BA.2-like) BA.2 Omicron Usher placements: BA.2(2/2)
Coinfection-nanopore2020-2%-error-20%-minor-variant 99.4% BA.2 Probable Omicron (Unassigned) BA.2 Omicron Usher placements: BA.2(3/3); scorpio found insufficient support to assign a specific lineage
Coinfection-nanopore2020-20%-error-2%-minor-variant 98.62% BA.2 Omicron (Unassigned) BA.2 Omicron Usher placements: BA.2(1/1); scorpio found insufficient support to assign a specific lineage

Freyja

The Freyja plot shows the relative SARS-CoV-2 lineage abundance in each sample. Samples suspect for coinfection will illustrate mixed prevalence of two or more variants. The plots below shows the summarized and specific lineages and their corresponding abundance as detected by Freyja.

VirStrain

Samples were analyzed using the VirStrain tool against a database of representative SARS-CoV-2 sequences. The results are summarized in the table below, where the ‘Most Possible Strain’ represents the lineage with the highest Vscore in the initial iteration. Meanwhile, the ‘Other Possible Strain’ is identified by the highest Vscore in subsequent iterations.

Sample Most Possible Strain Other Possible Strain Valid Map Rate
Coinfection-nanopore2020-5%-error-50%-minor-variant AY.25_B.1.617.2 Omicron 7/93
Coinfection-nanopore2020-2%-error-2%-minor-variant Omicron_BA.2 N10 2/93
Coinfection-nanopore2020-20%-error-10%-minor-variant Omicron_BA.2 AY.25 4/93
Coinfection-nanopore2020-20%-error-2%-minor-variant Omicron_BA.2 AY.25 4/93
Coinfection-nanopore2020-2%-error-50%-minor-variant AY.25_B.1.617.2 Omicron 7/93
Coinfection-nanopore2020-20%-error-5%-minor-variant Omicron_BA.2 Omicron 2/93
Coinfection-nanopore2020-10%-error-50%-minor-variant Omicron_BA.2 AY.25 8/93
Coinfection-nanopore2020-5%-error-20%-minor-variant Omicron_BA.2 AY.25 8/93
Coinfection-nanopore2020-10%-error-5%-minor-variant Omicron_BA.2 B.1.637 6/93
Coinfection-nanopore2020-10%-error-10%-minor-variant Omicron_BA.2 B.1.1.519 5/93
Coinfection-nanopore2020-10%-error-2%-minor-variant Omicron_BA.2 Omicron 1/93
Coinfection-nanopore2020-2%-error-10%-minor-variant Omicron_BA.2 AY.25 7/93
Coinfection-nanopore2020-5%-error-5%-minor-variant Omicron_BA.2 B.1.1.519 2/93
Coinfection-nanopore2020-5%-error-2%-minor-variant Omicron_BA.2 Omicron 1/93
Coinfection-nanopore2020-20%-error-20%-minor-variant Omicron_BA.2 AY.25 8/93
Coinfection-nanopore2020-10%-error-20%-minor-variant Omicron_BA.2 AY.25 8/93
Coinfection-nanopore2020-2%-error-5%-minor-variant Omicron_BA.2 Can not detect other strains. NA
Coinfection-nanopore2020-20%-error-50%-minor-variant AY.25_B.1.617.2 Omicron 7/93
Coinfection-nanopore2020-5%-error-10%-minor-variant Omicron_BA.2 AY.25 7/93
Coinfection-nanopore2020-2%-error-20%-minor-variant Omicron_BA.2 AY.25 8/93

Nucleotide mixture per position

The figure below shows the bammix plot for nucleotide mixtures of the sample/s with potential SARS-CoV-2 variants coinfection. Multiple sites containing heterogenous bases crossing the set threshold (default >20% minor alelle) mixture will be apparent.

Alternative allele fraction

For each lineage-defining mutations

The alternative allele fraction (AAF) determines the number of reads supporting each variant detected in the sample/s. The AAF per mutation of sample/s flagged for SARS-CoV-2 coinfection are shown in the figure.

For each amplicon

The AAF for each amplicon is plotted by getting the average allele fraction for each lineage within the range of that amplicon.

Amplicon sorting

Sample Coverage Pangolin Scorpio Nextclade WHO clade Note
Coinfection-nanopore2020-10%-error-50%-minor-variant_lineage_A 99.71% B.1.1.529 NA B.1 NA Usher placements: B.1.1.529(1/2) B.1.617.2(1/2)
Coinfection-nanopore2020-10%-error-50%-minor-variant_lineage_B 99.71% B.1.1.529 NA B.1 NA Usher placements: B.1.1.529(1/2) B.1.617.2(1/2)
Coinfection-nanopore2020-2%-error-20%-minor-variant_lineage_A 99.81% B.1.1.529 Probable Omicron (Unassigned) B.1 NA Usher placements: B.1.1.529(1/2) BA.2(1/2); scorpio found insufficient support to assign a specific lineage
Coinfection-nanopore2020-2%-error-20%-minor-variant_lineage_B 99.94% BA.2 Omicron (Unassigned) BA.2.23 Omicron Usher placements: BA.2(2/2); scorpio found insufficient support to assign a specific lineage
Coinfection-nanopore2020-20%-error-50%-minor-variant_lineage_A 99.79% B.1.617.2 NA B.1 NA Usher placements: AY.1(1/20) B.1.617.2(19/20)
Coinfection-nanopore2020-20%-error-50%-minor-variant_lineage_B 99.71% B.1.1.529 NA B.1 NA Usher placements: B.1.1.529(1/4) B.1.617.2(3/4)
Coinfection-nanopore2020-10%-error-20%-minor-variant_lineage_A 99.75% B.1.1.529 NA B.1 NA Usher placements: B.1.1.529(1/1)
Coinfection-nanopore2020-10%-error-20%-minor-variant_lineage_B 99.86% BA.2 Probable Omicron (Unassigned) B.1.1 NA Usher placements: BA.2(2/2); scorpio found insufficient support to assign a specific lineage
Coinfection-nanopore2020-5%-error-10%-minor-variant_lineage_A 99.86% BA.2 Omicron (Unassigned) B.1.1 NA Usher placements: BA.2(10/10); scorpio found insufficient support to assign a specific lineage
Coinfection-nanopore2020-5%-error-10%-minor-variant_lineage_B 99.95% BA.2 Omicron (Unassigned) BA.2 Omicron Usher placements: BA.2(1/1); scorpio found insufficient support to assign a specific lineage
Coinfection-nanopore2020-2%-error-10%-minor-variant_lineage_A 99.91% BA.2 Probable Omicron (Unassigned) XAP recombinant Usher placements: BA.2(1/1); scorpio found insufficient support to assign a specific lineage
Coinfection-nanopore2020-2%-error-10%-minor-variant_lineage_B 99.97% BA.2 Omicron (BA.2-like) BA.2 Omicron Usher placements: BA.2(1/1)
Coinfection-nanopore2020-10%-error-10%-minor-variant_lineage_A 99.91% BA.2 Omicron (Unassigned) B.1.1.529 Omicron Usher placements: BA.2(1/1); scorpio found insufficient support to assign a specific lineage
Coinfection-nanopore2020-10%-error-10%-minor-variant_lineage_B 99.97% BA.2 Omicron (BA.2-like) BA.2 Omicron Usher placements: BA.2(1/1)
Coinfection-nanopore2020-10%-error-2%-minor-variant_lineage_A 99.98% BA.2 Omicron (BA.2-like) BA.2 Omicron Usher placements: BA.2(4/4)
Coinfection-nanopore2020-10%-error-2%-minor-variant_lineage_B 100.0% BA.2 Omicron (BA.2-like) BA.2 Omicron Usher placements: BA.2(2/2)
Coinfection-nanopore2020-2%-error-50%-minor-variant_lineage_A 99.7% B.1.1.529 NA B.1 NA Usher placements: AY.1(1/28) B.1.1.529(1/28) B.1.617.2(26/28)
Coinfection-nanopore2020-2%-error-50%-minor-variant_lineage_B 99.7% B.1.1.529 NA B.1 NA Usher placements: AY.1(1/28) B.1.1.529(1/28) B.1.617.2(26/28)
Coinfection-nanopore2020-5%-error-50%-minor-variant_lineage_A 99.73% B.1.1.529 NA B.1 NA Usher placements: AY.1(1/28) B.1.1.529(1/28) B.1.617.2(26/28)
Coinfection-nanopore2020-5%-error-50%-minor-variant_lineage_B 99.7% B.1.1.529 NA B.1 NA Usher placements: B.1.1.529(1/1)
Coinfection-nanopore2020-5%-error-20%-minor-variant_lineage_A 99.72% B.1.1.529 NA B.1 NA Usher placements: B.1.1.529(1/1)
Coinfection-nanopore2020-5%-error-20%-minor-variant_lineage_B 99.82% BA.2 Probable Omicron (Unassigned) B.1.1 NA Usher placements: BA.2(1/1); scorpio found insufficient support to assign a specific lineage
Coinfection-nanopore2020-20%-error-20%-minor-variant_lineage_A 99.78% B.1.617.2 Delta (B.1.617.2-like) B.1 NA Usher placements: B.1(1/3) B.1.617.2(2/3)
Coinfection-nanopore2020-20%-error-20%-minor-variant_lineage_B 99.83% BA.2 Probable Omicron (Unassigned) B.1.1 NA Usher placements: BA.2(1/1); scorpio found insufficient support to assign a specific lineage
Coinfection-nanopore2020-20%-error-10%-minor-variant_lineage_A 99.93% BA.2 Omicron (Unassigned) BA.2 Omicron Usher placements: BA.2(5/5); scorpio found insufficient support to assign a specific lineage
Coinfection-nanopore2020-20%-error-10%-minor-variant_lineage_B 99.99% BA.2 Omicron (BA.2-like) BA.2 Omicron Usher placements: BA.2(5/5)

References

The tools used in this pipeline are as follows: